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Of all publications in the section: 3
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Article
Akparov V., Timofeev V., Khaliullin I. et al. Journal of Biomolecular Structure and Dynamics. 2018. Vol. 36. No. 15. P. 3958-3966.

Recently, we have investigated the three-dimensional structures of CPT in complexes with the ground-state substrate analogs carrying hydrophobic and positively charged side chains: benzylsuccinic acid (BZS) and S-(2-guanidinoethylmercapto)succinic acid (GEMSA). That allowed us to identify Leu211 and Leu254 – earlier unknown determinants of substrate recognition by CPT as density of their interaction with substrates and localization of their side chains in the S1′-subsite were dependent on substrate’s structure. The role of Leu211 and Leu254 as structure determinants of hydrophobic selectivity of CPT was confirmed by site-directed mutagenesis. In the present work, we compare the structural organization of the CPT active site in complexes with transition state analogs of phenylalanine and arginine-containing substrates to evaluate structural basis of the enzyme’s catalytic activity to a broad range of substrates.

Added: Jan 28, 2019
Article
Pyrkova D. V., Tarasova N. K., Krylov N. et al. Journal of Biomolecular Structure and Dynamics. 2013. Vol. 31. No. 1. P. 87-95.

Delineation and analysis of lateral clustering of lipids in model bilayers is an important step toward understanding of the physical processes underlying formation of lipid domains and rafts in cell membranes. Computer modeling methods represent a powerful tool to address the problem since they can detect clusters of only few lipid molecules – this issue still resists easy characterization with modern experimental techniques. In this work, we propose a computational method to detect and analyze parts of membrane with different packing densities and hydrogen bonding patterns. A series of one- and two-component fluid systems containing lipids with the same polar heads and different acyl chains, dioleoylphosphatidylcholine (18:1) and dipalmitoylphosphatidylcholine (16:0), or with same acyl chains and different polar heads, dioleoylphosphatidylserine (18:1) and dioleoylphosphatidylcholine (18:1), were studied via molecular dynamics simulations. Four criteria of clustering were considered. It was shown that the water-lipid interface of biomembranes represents a highly dynamic and “mosaic” picture, whose parameters depend on the bilayer composition. Some systems (e.g., with 20-30% of the anionic lipid) demonstrate unusual clustering properties and demand further investigation at molecular level. Lateral microheterogeneities in fluid lipid bilayers seem to be among the most important factors determining the nature of the membrane-water interface in a cell.

Added: Nov 14, 2013
Article
Akparov V., Timofeev V., Khaliullin I. et al. Journal of Biomolecular Structure and Dynamics. 2018. Vol. 36. No. 4. P. 956-965.

Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However, its ability to discriminate substrates with hydrophobic, hydrophilic, and charged side chains is not well understood. We report structure of CPB complex with a transition state analog N-sulfamoyl-L-phenylalanine solved at 1.74 angstrom. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center. Side chain of the non-specific substrate analog SPhe in comparison with that of specific substrate analog SArg (reported earlier) not only loses favorable electrostatic interactions and two hydrogen bonds with Asp255 and three fixed water molecules, but is forced to be in the unfavorable hydrophilic environment. Thus, Ser207, Gly253, Tyr248, and Asp255 residues play major role in the substrate recognition by S1'-subsite.

Added: Jan 28, 2019